Contacts of the helix formed by residues 333 - 341 (chain H) in PDB entry 2HOI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 333 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328H LEU* 6.2 1.6 - - - -
329H ASP 3.2 11.6 + - - -
330H SER* 2.9 17.8 + - - -
331H GLU 3.4 0.2 - - - -
332H THR* 1.3 83.5 - - - +
334H ALA* 1.3 67.2 + - - -
335H MET 3.3 3.4 + - - -
336H VAL* 3.6 2.7 + - - -
337H ARG* 3.3 21.2 + - - +
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Residues in contact with ALA 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G MET* 4.0 13.7 - - - -
304G VAL* 3.9 38.2 - - + +
308G GLU* 5.2 11.3 + - + +
312G ALA* 5.6 2.4 - - + +
333H GLY* 1.3 70.7 - - - -
335H MET* 1.3 58.0 + - + +
337H ARG* 3.5 18.9 + - - +
338H LEU* 3.0 32.5 + - - +
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Residues in contact with MET 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G TYR* 3.3 51.6 - - + +
169G ASN* 3.5 22.0 - - - +
171G LEU* 3.6 18.8 - - + -
295G ALA* 3.9 13.5 - - + +
299G MET* 3.7 39.3 - - - +
312G ALA* 4.7 6.3 - - + +
333H GLY 3.3 0.6 + - - -
334H ALA* 1.3 75.2 - - - +
336H VAL* 1.3 61.3 + - + +
338H LEU* 3.3 11.5 + - + +
339H LEU* 3.0 33.5 + - + +
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Residues in contact with VAL 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G ASN* 4.1 3.8 - - - +
192G ARG* 3.9 9.6 - - - +
212G ALA* 3.5 31.9 - - + +
213G LEU 4.0 1.1 - - - +
214G SER* 4.0 19.7 - - - +
330H SER 3.8 17.0 + - - +
331H GLU 3.3 23.3 - - - +
333H GLY 3.6 2.1 + - - +
334H ALA 3.5 0.2 - - - -
335H MET* 1.3 76.9 - - + +
337H ARG* 1.3 63.2 + - + +
339H LEU* 3.4 1.2 + - - +
340H GLU* 3.1 50.1 + - - +
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Residues in contact with ARG 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304G VAL* 5.4 7.1 - - - +
308G GLU* 5.1 11.1 + - - -
301H ARG* 6.2 2.4 - - - +
331H GLU 5.2 1.1 - - - +
332H THR* 2.9 35.5 + - - +
333H GLY* 3.3 21.3 + - - +
334H ALA* 3.8 13.4 - - - +
335H MET 3.3 0.6 - - - -
336H VAL* 1.3 76.6 - - + +
338H LEU* 1.3 61.4 + - - +
340H GLU* 4.2 3.0 - - - +
341H ASP* 3.3 26.7 + - - +
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Residues in contact with LEU 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ARG* 2.8 21.9 + - - +
168G TYR* 5.2 2.9 - - - +
298G ASP* 4.0 13.0 - - + +
299G MET* 3.6 46.7 - - + +
302G ALA* 3.8 24.2 - - + -
304G VAL* 5.0 3.1 - - + -
334H ALA 3.0 16.4 + - - +
335H MET* 3.5 17.3 - - + +
337H ARG* 1.3 77.6 - - - +
339H LEU* 1.3 58.3 + - + +
341H ASP 2.9 16.4 - - - +
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Residues in contact with LEU 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ARG* 3.4 38.7 + - - +
142G PHE* 4.3 17.7 - - + -
146G ARG* 4.7 5.2 - - - +
168G TYR* 3.8 34.5 - - + -
169G ASN* 3.5 40.8 - - + +
214G SER* 3.8 20.6 - - - +
217G VAL* 4.2 4.7 - - + -
335H MET* 3.0 19.1 + - + +
336H VAL 4.0 0.2 - - - +
337H ARG 3.3 0.2 - - - -
338H LEU* 1.3 78.3 - - + +
340H GLU* 1.3 63.3 + - - +
341H ASP 3.5 0.2 - - - -
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Residues in contact with GLU 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G ARG* 2.7 47.5 + - - -
214G SER* 3.4 13.6 - - - -
215G LEU* 2.8 31.5 + - + +
216G GLY 5.2 2.0 - - - +
336H VAL* 3.1 23.8 + - - +
337H ARG* 4.5 2.8 - - - +
339H LEU* 1.3 77.6 - - - +
341H ASP* 1.3 75.8 + - - +
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Residues in contact with ASP 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ARG* 4.2 5.0 + - - +
337H ARG 3.3 13.6 + - - +
338H LEU* 2.9 23.2 - - - +
339H LEU 3.5 0.4 - - - -
340H GLU* 1.3 89.4 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il